breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors28-88-m-tartrate_S16_L001_R1_001.good.fq1,242,583341,877,506100.0%275.1 bases289 bases99.3%
errors28-88-m-tartrate_S16_L001_R2_001.good.fq1,242,583342,613,403100.0%275.7 bases289 bases80.7%
total2,485,166684,490,909100.0%275.4 bases289 bases90.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652128.73.4100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000002672
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000198
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.025

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86033

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input21:32:25 26 Mar 201921:33:15 26 Mar 201950 seconds
Read alignment to reference genome21:33:15 26 Mar 201921:50:40 26 Mar 201917 minutes 25 seconds
Preprocessing alignments for candidate junction identification21:50:40 26 Mar 201921:51:22 26 Mar 201942 seconds
Preliminary analysis of coverage distribution21:51:22 26 Mar 201921:53:40 26 Mar 20192 minutes 18 seconds
Identifying junction candidates21:53:40 26 Mar 201921:53:44 26 Mar 20194 seconds
Re-alignment to junction candidates21:53:44 26 Mar 201921:56:55 26 Mar 20193 minutes 11 seconds
Resolving best read alignments21:56:55 26 Mar 201921:58:08 26 Mar 20191 minute 13 seconds
Creating BAM files21:58:08 26 Mar 201922:00:04 26 Mar 20191 minute 56 seconds
Tabulating error counts22:00:04 26 Mar 201922:01:00 26 Mar 201956 seconds
Re-calibrating base error rates22:01:00 26 Mar 201922:01:01 26 Mar 20191 second
Examining read alignment evidence22:01:01 26 Mar 201922:11:20 26 Mar 201910 minutes 19 seconds
Polymorphism statistics22:11:20 26 Mar 201922:11:20 26 Mar 20190 seconds
Output22:11:20 26 Mar 201922:11:36 26 Mar 201916 seconds
Total 39 minutes 11 seconds